setJitterFrac<-function(dir,frac=0.1){
res=scan(file.path(dir,"/starter.ss"),
what=as.character(),sep="\n")
res=paste(str_trim(res)," ")
res=res[!substr(res,1,1)=="#"]
res2=maply(res[-c(1:2,length(res))],function(x) substr(x,1,gregexpr("\\s",x)[[1]][1]-1))
res2[13]=frac
cat(c(res[1:2],res2,"999"),sep="\n",file=file.path(dir,"starter.ss"))}
jitterSS<-function(dir,frac=0.1){
dirNow=getwd()
#create temp dir
dirTmp=mkTmp()
#copy from target to temp
system(paste("cp",file.path(dir,"*.*"),dirTmp))
setwd(dirTmp)
#set jitter
setJitterFrac(dirTmp,frac=frac)
#run
system2("./ss3_3.24z",stdout=NULL)
#get results
res=try(SS_output(dirTmp,verbose=FALSE,printstats=FALSE))
#clean up
setwd(dirNow)
if (is(res)=="try-error")
NULL
else{
rmTmp(dirTmp)
res}
}
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